Variant report

Variant	rs4622250
Chromosome Location	chr11:3918601-3918602
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10160703	1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10767679	1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10767680	1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10767681	1.00[JPT][hapmap]
rs10767695	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10835232	1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10835236	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs10835239	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10835249	1.00[JPT][hapmap]
rs10835262	1.00[CEU][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs10835270	0.88[MEX][hapmap];0.84[TSI][hapmap]
rs11030122	1.00[CEU][hapmap]
rs11030209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11030211	0.86[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs1869084	1.00[CEU][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1869085	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs4414209	0.95[CEU][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap]
rs4457735	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4584571	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4598668	0.85[JPT][hapmap]
rs4910584	1.00[JPT][hapmap]
rs4910859	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7111609	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7113148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7131437	1.00[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1051580	chr11:3856201-3924216	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
9	nsv1043265	chr11:3856201-3926407	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
10	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv1051904	chr11:3903226-3939186	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv1050077	chr11:3903226-3940726	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv1043039	chr11:3903226-3955159	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4622250	TRIM21	cis	cerebellum	SCAN
rs4622250	OR51G2	cis	parietal	SCAN
rs4622250	CD81	cis	parietal	SCAN
rs4622250	IFITM3	cis	parietal	SCAN
rs4622250	RRM1	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3899200-3926200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr11:3902400-3923800	Weak transcription	Gastric	stomach
3	chr11:3907400-3923600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:3907600-3922600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:3913400-3918800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr11:3915800-3923800	Weak transcription	HMEC	breast
7	chr11:3915800-3924000	Weak transcription	HepG2	liver
8	chr11:3916000-3921400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:3916000-3921800	Weak transcription	Thymus	Thymus
10	chr11:3916000-3922800	Weak transcription	Colonic Mucosa	Colon
11	chr11:3916200-3918800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr11:3916400-3921400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:3916400-3921400	Weak transcription	Psoas Muscle	Psoas
14	chr11:3916600-3921400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:3916600-3921400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr11:3916600-3921400	Weak transcription	Left Ventricle	heart
17	chr11:3916600-3921400	Weak transcription	Spleen	Spleen
18	chr11:3916600-3921600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:3916600-3921600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr11:3916600-3921600	Weak transcription	Lung	lung
21	chr11:3916600-3921800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr11:3916600-3921800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr11:3916600-3922000	Weak transcription	Primary T cells from cord blood	blood
24	chr11:3916600-3922000	Weak transcription	Fetal Thymus	thymus
25	chr11:3916600-3922800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr11:3916600-3923000	Weak transcription	Placenta	Placenta
27	chr11:3916600-3923000	Weak transcription	Pancreas	Pancrea
28	chr11:3916600-3923800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:3916600-3923800	Weak transcription	Adipose Nuclei	Adipose
30	chr11:3916600-3923800	Weak transcription	Fetal Muscle Leg	muscle
31	chr11:3916600-3923800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr11:3916600-3924400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:3916600-3925400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr11:3916600-3925800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:3916600-3943800	Weak transcription	Fetal Stomach	stomach
36	chr11:3916600-3948800	Weak transcription	Aorta	Aorta
37	chr11:3916800-3921400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr11:3916800-3921400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr11:3916800-3921400	Weak transcription	Right Ventricle	heart
40	chr11:3916800-3921800	Weak transcription	K562	blood
41	chr11:3916800-3922200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:3916800-3922400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr11:3916800-3922600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:3916800-3922800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr11:3916800-3925400	Weak transcription	Fetal Lung	lung
46	chr11:3918000-3918800	Enhancers	Primary B cells from cord blood	blood
47	chr11:3918000-3921400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr11:3918000-3921600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr11:3918400-3918800	ZNF genes & repeats	GM12878-XiMat	blood
50	chr11:3918400-3921400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links